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Database: cavPor3 Primary Table: ncbiRefSeq Row Count: 44,775   Data last updated: 2020-04-01
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | NP_008751.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | chrM | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 2720 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 3680 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 2720 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 3680 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 1 | int(10) unsigned | range | Number of exons |
exonStarts | 2720, | longblob | | Exon start positions (or end positions for minus strand item) |
exonEnds | 3680, | longblob | | Exon end positions (or start positions for minus strand item) |
score | 0 | int(11) | range | score |
name2 | ND1 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
exonFrames | 0, | longblob | | Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region. |
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Connected Tables and Joining Fields
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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585 | NP_008751.1 | chrM | + | 2720 | 3680 | 2720 | 3680 | 1 | 2720, | 3680, | 0 | ND1 | cmpl | cmpl | 0, |
585 | NP_008752.1 | chrM | + | 3886 | 4930 | 3886 | 4930 | 1 | 3886, | 4930, | 0 | ND2 | cmpl | cmpl | 0, |
585 | NP_008753.1 | chrM | + | 5328 | 6870 | 5328 | 6870 | 1 | 5328, | 6870, | 0 | COX1 | cmpl | cmpl | 0, |
585 | NP_008754.1 | chrM | + | 7017 | 7701 | 7017 | 7701 | 1 | 7017, | 7701, | 0 | COX2 | cmpl | cmpl | 0, |
585 | NP_008755.1 | chrM | + | 7769 | 7973 | 7769 | 7973 | 1 | 7769, | 7973, | 0 | ATP8 | cmpl | cmpl | 0, |
585 | NP_008756.1 | chrM | + | 7930 | 8611 | 7930 | 8611 | 1 | 7930, | 8611, | 0 | ATP6 | cmpl | cmpl | 0, |
585 | NP_008757.1 | chrM | + | 8610 | 9394 | 8610 | 9394 | 1 | 8610, | 9394, | 0 | COX3 | cmpl | cmpl | 0, |
585 | NP_008758.1 | chrM | + | 9462 | 9808 | 9462 | 9808 | 1 | 9462, | 9808, | 0 | ND3 | cmpl | cmpl | 0, |
585 | NP_008759.1 | chrM | + | 9878 | 10175 | 9878 | 10175 | 1 | 9878, | 10175, | 0 | ND4L | cmpl | cmpl | 0, |
585 | NP_008760.1 | chrM | + | 10168 | 11546 | 10168 | 11546 | 1 | 10168, | 11546, | 0 | ND4 | cmpl | cmpl | 0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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